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Aim In deserts, past climate change (and particularly past rainfall variability) plays a large role in explaining current plant species distributions. We ask which species were most and which were least affected by changes in rainfall during the late Quaternary in northernmost Chile. Location Quebrada La Higuera ( QLH; 18° S), a shallow canyon that cuts east-west through the western Andean precordillera of northern Chile, connecting the Altiplano with the hyperarid Atacama Desert. Methods We collected and dated 22 rodent middens from elevations of 3100-3500 m in QLH. These were analysed for identifiable plant macrofossils and pollen. We also measured chinchilla rat ( Abrocoma cinerea) faecal pellets in the youngest middens to explore how they relate to past ecological and climatic change. Results The three oldest middens dated to more than 37 ka (thousand calibrated 14C years), four middens dated to 14.4-11.6 ka, and fifteen middens spanned the last 650 years. During all the intervals examined, extralocal species (those found today at higher elevations and indicative of positive rainfall anomalies) were present at our midden sites. In the youngest interval, Parastrephia pollen (indicating increased rainfall) increased abruptly at ad 1760 and remained high until the mid-1800s. This increase was also seen in our faecal pellet record. Main conclusions Extralocal species were prevalent in late Pleistocene middens at lower elevations when the climate was wetter. When combined with other regional midden records, we postulate that many species found today in the Altiplano were displaced to lower elevations during the late Pleistocene. The recent large-scale mortality documented among arboreal cactus populations along the present upper margins of the Atacama suggests that these are relict populations that are likely to have flourished during a wetter period in the early 1800s. [ABSTRACT FROM AUTHOR]